#Created by Kbib version 0.6.4
#Last modified: Wed Jul 15 20:58:51 2009

@article{ Ruehle:2009.a,
  author    = {V. R\"uhle and C. Junghans and A. Lukyanov and K. Kremer and D. Andrienko},
  title     = {Versatile Object-oriented Toolkit for Coarse-graining Applications},
  journal   = {J. Chem. Theor. Comp.},
  year      = {2009},
  volume    = {5},
  pages     = {3211},
  condmat   = {},
  doi       = {10.1021/ct900369w},
  abstract  = {}
}


@article{Ruehle:2008,
	author = {V. R\"uhle and J. Kirkpatrick and K. Kremer and D. Andrienko},
	title = {Coarse-grained modelling of polypyrrole morphologies},
	journal = {Phys. Stat. Solidi B},
	year = {2008},
	volume = {245},
	pages = {844},
	doi = {10.1002/pssb.200743443},
	abstract = {A multiscale model to simulate large scale morphologies and study charge transport in
polypyrrole is developed. First, {\em ab-i
nitio} methods are used to derive an atomistic force field. Coarse graining of this atomistic model is then
performed. At a fina
l stage, the analysis of simulated morphologies allows to split polymer chains into conjugated segments, which
can further be us
ed to simulate both inter- and intrachain charge dynamics.},

}

@article{Lyubartsev:1995,
	author = {Lyubartsev, Ap And Laaksonen, A},
	title = {Calculation Of Effective Interaction Potentials From Radial-Distribution Functions - A Reverse Monte-Carlo Approach},
	journal = {Phys. Rev. E},
	year = 1995,
	volume = {52},
	number = 4,
	pages = {3730-3737},
	abstract = {An approach is presented to solve the reverse problem of statistical mechanics: reconstruction of interaction potentials from radial distribution functions. The method consists of the iterative adjustment of the interaction potential to known radial distribution functions using a Monte Carlo simulation technique and statistical-mechanics relations to connect deviations of canonical averages with Hamiltonian parameters. The method is applied to calculate the effective interaction potentials between the ions in aqueous NaCl solutions at two different concentrations. The reference ion-ion radial distribution functions, calculated in separate molecular dynamics simulations with water molecules, are reproduced in Monte Carlo simulations, using the effective interaction potentials for the hydrated ions. Application of the present method should provide an effective and economical way to simulate equilibrium properties for very large molecular systems (e.g., polyelectrolytes) in the presence of hydrated ions, as well as to offer an approach to reduce a complexity in studies of various associated and aggregated systems in solution.},

}

@article{Soper:1996,
	author = {Soper, AK},
	title = {Empirical potential Monte Carlo simulation of fluid structure},
	journal = {Chem. Phys.},
	year = 1996,
	volume = {202},
	pages = {295-306},
	abstract = {It is shown that data on the site-site pair correlation functions for a fluid of molecules can be used to derive a set of empirical site-site potential energy functions. These potential functions reproduce the fluid structure accurately but at the present time do not reproduce thermodynamic information on the fluid, such as the internal energy or pressure. The method works in an iterative manner, starting from a reference fluid in which only Lennard-Jones interactions are included, and generates, by Monte Carlo simulation, successive corrections to those potentials which eventually lead to the correct site-site pair correlation functions. Using this approach the structure of water as determined from neutron scattering experiments is compared to the structure of water obtained from the simple point charge extended (SPCE) model of water interactions. The empirical potentials derived from both experiment and SPCE water show qualitative similarities with the true SPCE potential, although there are quantitative differences. The simulation is driven by a set of potential energy functions, with equilibration of the energy of the distribution, and not, as in the reverse Monte Carlo method, by equilibrating the value of chi(2), which measures how closely the simulated site-site pair correlation functions fit a set of diffraction data. As a result the simulation proceeds on a true random walk and samples a wide range of possible molecular configurations.},

}

@article{Tschoep:1998,
	author = {Tsch{\"o}p, W and Kremer, K and Batoulis, J and Burger, T and Hahn, O},
	title = {Simulation of polymer melts. I. Coarse-graining procedure for polycarbonates},
	journal = {Acta Polymerica},
	year = 1998,
	volume = {49},
	pages = {61-74},
	abstract = {The paper introduces a systematic procedure to coarse grain atomistic polymer models into a mesoscopic model, which then allows an effective and fast simulation of melts. The method, which provides information on both static and dynamic properties, is tested for three different modifications of polycarbonate. The models successfully describe the variation in the Vogel-Fulcher temperature as well as the total chain extension. The effective speedup compared to the corresponding atomistic simulation is significantly above 10(3).},

}

@article{Reith:2003,
	author = {Reith, D and P{\"u}tz, M and M{\"u}ller-Plathe, F},
	title = {Deriving effective mesoscale potentials from atomistic simulations},
	journal = {J. Comp. Chem.},
	year = 2003,
	volume = {24},
	number = 13,
	pages = {1624-1636},
	doi = {10.1002/jcc.10307},
	abstract = {We demonstrate how an iterative method for potential inversion from distribution functions developed for simple liquid systems can be generalized to polymer systems. It uses the differences in the potentials of mean force between the distribution functions generated from a guessed potential and the true distribution functions to improve the effective potential successively. The optimization algorithm is very powerful: convergence is reached for every trial function in few iterations. As an extensive test case we coarse-grained an atomistic all-atom model of polyisoprene (PI) using a 13:1 reduction of the degrees of freedom. This procedure was performed for PI solutions as well as for a PI melt. Comparisons of the obtained force fields are drawn. They prove that it is not possible to use a single force field for different concentration regimes. (C) 2003 Wiley Periodicals, Inc.},

}

@article{Plathe:2002,
	author = {M{\"u}ller-Plathe, Florian},
	title = {Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back.},
	journal = {Chemphyschem},
	year = 2002,
	volume = {3},
	number = 9,
	pages = {755--769},
	abstract = {Polymers can be theoretically and computationally described by models pertaining to different length scales and corresponding time scales. These models have traditionally been used independently of each other. Recently, considerable progress has been made in systematically linking models of different scales. This Review focuses on the generation of lattice and off-lattice coarse-grained polymer models, whose ``monomers'' correspond to roughly a chemical repeat unit, from chemically detailed atomistic simulations of the same polymers. Computational methods are described as well as applications to polymers in the melt and in solution. The success of multiscale simulations in solving real-world polymer problems that could not be solved in any other way suggests that they will have an important role to play in the future.},

}

@article{Abrams:2003,
	author = {Abrams, CF and Kremer, K},
	title = {Combined coarse-grained and atomistic simulation of liquid bisphenol A-polycarbonate: Liquid packing and intramolecular structure},
	journal = {Macromolecules},
	year = 2003,
	volume = {36},
	number = 1,
	pages = {260-267},
	doi = {10.1021/ma0213495},
	abstract = {We present a new coarse-graining scheme for efficient molecular dynamics simulations of polycarbonate liquids and compare its effectiveness to that of a previously presented model which uses a different coarse-grained representation. The effect of more realistically accounting for the excluded volume of the phenylene comonomeric units in the coarse-grained simulation is examined. The new treatment avoids artifacts arising from sphere-packing, which dominate the liquid structure and dynamics in the older scheme, leading to a significant improvement in the equilibration time, for systems run at the typical processing temperature of 570 K. However, we observe only a slight improvement (10(-4) eV/atom) in the equilibration of atomistically detailed samples that are inverse-mapped from the equilibrated coarse-grained configurations. Distributions in the atomistically resolved backbone bond and torsion angles are identical using the two schemes, as are computed liquid coherent scattering functions. This indicates that artifacts present at the coarsened level are effectively erased by equilibration at full-blown atomistic resolution, at least for systems with relatively short chains well above the glass transition temperature.},

}

@article{Ercolessi:1994,
	author = {Ercolessi, F. and Adams, J. B.},
	title = {Interatomic Potentials from 1st-Principles Calculations - the Force-Matching Method},
	journal = {Europhys. Lett.},
	year = 1994,
	volume = {26},
	number = 8,
	pages = {583-588},
	abstract = {We present a new scheme to extract numerically <<optimal>> interatomic potentials from large amounts of data produced by first-principles calculations. The method is based on fitting the potential to ab initio atomic forces of many atomic configurations, including surfaces, clusters, liquids and crystals at finite temperature. The extensive data set overcomes the difficulties encountered by traditional fitting approaches when using rich and complex analytic forms, allowing to construct potentials with a degree of accuracy comparable to that obtained by ab initio methods. A glue potential for aluminium obtained with this method is presented and discussed.},

}

@article{Izvekov:2004,
	author = {Izvekov, S. and Parrinello, M. and Burnham, C. J. and Voth, G. A.},
	title = {Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: A new method for force-matching},
	journal = {J. Chem. Phys.},
	year = {2004},
	volume = {120},
	number = {23},
	pages = {10896-10913},
	abstract = {A novel least-squares fitting approach is presented to obtain classical force fields from trajectory and force databases produced by ab initio (e.g., Car-Parrinello) molecular dynamics (MD) simulations. The method was applied to derive effective nonpolarizable three-site force fields for liquid water at ambient conditions from Car-Parrinello MD simulations in the Becke-Lee-Yang-Parr approximation to the electronic density functional theory. The force-matching procedure includes a fit of short-ranged nonbonded forces, bonded forces, and atomic partial charges. The various parameterizations of the water force field differ by an enforced smooth cut-off applied to the short-ranged interaction term. These were obtained by fitting to the trajectory and force data produced by Car-Parrinello MD simulations of systems of 32 and 64 H2O molecules. The new water force fields were developed assuming both flexible or rigid molecular geometry. The simulated structural and self-diffusion properties of liquid water using the fitted force fields are in close agreement with those observed in the underlying Car-Parrinello MD simulations. The resulting empirical models compare to experiment much better than many conventional simple point charge (SPC) models. The fitted potential is also shown to combine well with more sophisticated intramolecular potentials. Importantly, the computational cost of the new models is comparable to that for SPC-like potentials. (C) 2004 American Institute of Physics.},

}

@article{Izvekov:2005,
	author = {Izvekov, S and Voth, GA},
	title = {Multiscale coarse graining of liquid-state systems},
	journal = {J. Chem. Phys.},
	year = 2005,
	volume = {123},
	number = 13,
	pages = {134105},
	month = {OCT 1},
	doi = {10.1063/1.2038787},
	abstract = {A methodology is described to systematically derive coarse-grained (CG) force fields for molecular liquids from the underlying atomistic-scale forces. The coarse graining of an interparticle force field is accomplished by the application of a force-matching method to the trajectories and forces obtained from the atomistic trajectory and force data for the CG sites of the targeted system. The CG sites can be associated with the centers of mass of atomic groups because of the simplicity in the evaluation of forces acting on these sites from the atomistic data. The resulting system is called a multiscale coarse-grained (MS-CG) representation. The MS-CG method for liquids is applied here to water and methanol. For both liquids one-site and two-site CG representations without an explicit treatment of the long-ranged electrostatics have been derived. In addition, for water a two-site model having the explicit long-ranged electrostatics has been developed. To improve the thermodynamic properties (e.g., pressure and density) for the MS-CG models, the constraint for the instantaneous virial was included into the force-match procedure. The performance of the resulting models was evaluated against the underlying atomistic simulations and experiment. In contrast with existing approaches for coarse graining of liquid systems, the MS-CG approach is general, relies only on the interatomic interactions in the reference atomistic system. (c) 2005 American Institute of Physics.},

}

@article{Murtola:2009,
	author = {Murtola, T. and Bunker, A. and Vattulainen, I. and Deserno, M. and Karttunen, M.},
	title = {Multiscale modeling of emergent materials: biological and soft matter},
	journal = {Phys. Chem. Chem. Phys.},
	year = {2009},
	volume = {11},
	number = {12},
	pages = {1869-1892},
	abstract = {In this review, we focus on four current related issues in multiscale modeling of soft and biological matter. First, we discuss how to use structural information from detailed models (or experiments) to construct coarse-grained ones in a hierarchical and systematic way. This is discussed in the context of the so-called Henderson theorem and the inverse Monte Carlo method of Lyubartsev and Laaksonen. In the second part, we take a different look at coarse graining by analyzing conformations of molecules. This is done by the application of self-organizing maps, i.e., a neural network type approach. Such an approach can be used to guide the selection of the relevant degrees of freedom. Then, we discuss technical issues related to the popular dissipative particle dynamics (DPD) method. Importantly, the potentials derived using the inverse Monte Carlo method can be used together with the DPD thermostat. In the final part we focus on solvent-free modeling which offers a different route to coarse graining by integrating out the degrees of freedom associated with solvent.},

}

@article{Tschoep:1998.2,
	author = {Tschop, W and Kremer, K and Hahn, O and Batoulis, J and Burger, T},
	title = {Simulation of polymer melts. II. From coarse-grained models back to atomistic description},
	journal = {Acta Polymerica},
	year = 1998,
	volume = {49},
	pages = {75-79},
	month = {FEB},
	url = {http://links.isiglobalnet2.com/gateway/Gateway.cgi?GWVersion=1&SrcAuth=KBib&SrcApp=KBib&KeyUT=000072137500002},
	abstract = {Starting out from a computer simulation of a rather simple bead spring model, where the parameters are determined from an atomistic model by a numerical renormalization procedure (preceeding paper), after long simulation runs the chemical details are reintroduced into the coarse-grained chains. The resulting microscopic structure is compared to neutron scattering results. The procedure is tested for two different polycarbonate modifications.},

}

@article{Noid:2008.1,
	author = {Noid, W G and Chu, J and Ayton, G S and Krishna, V and Izvekov, S and Voth, G and Das, A and Andersen, H C},
	title = {The multiscale coarse graining method. 1. A rigorous bridge between atomistic and coarse-grained models},
	journal = {J. Chem. Phys.},
	year = 2008,
	volume = {128},
	pages = {244114},
	month = {JUN},
	abstract = {Coarse-grained (CG) models provide a computationally efficient method for rapidly investigating the long time- and length-scale processes that play a critical role in many important biological and soft matter processes. Recently, Izvekov and Voth introduced a new multiscale coarse-graining (MS-CG) method [J. Phys. Chem. B 109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] for determining the effective interactions between CG sites using information from simulations of atomically detailed models. The present work develops a formal statistical mechanical framework for the MS-CG method and demonstrates that the variational principle underlying the method may, in principle, be employed to determine the many-body potential of mean force (PMF) that governs the equilibrium distribution of positions of the CG sites for the MS-CG models. A CG model that employs such a PMF as a ?potential energy function? will generate an equilibrium probability distribution of CG sites that is consistent with the atomically detailed model from which the PMF is derived. Consequently, the MS-CG method provides a formal multiscale bridge rigorously connecting the equilibrium ensembles generated with atomistic and CG models. The variational principle also suggests a class of practical algorithms for calculating approximations to this many-body PMF that are optimal. These algorithms use computer simulation data from the atomically detailed model. Finally, important generalizations of the MS-CG method are introduced for treating systems with rigid intramolecular constraints and for developing CG models whose equilibrium momentum distribution is consistent with that of an atomically detailed model. �2008 American Institute of Physics},

}

@article{Noid:2008.2,
	author = {Noid, W G and Liu, P and Wang, Y and Chu, J and Ayton, G and Izvekov, S and Andersen, H C and Voth, G},
	title = {The multiscale coarse-graining method. 2. Numerical implementation for coarse-grained molecular models},
	journal = {J. Chem. Phys.},
	year = 2008,
	volume = {128},
	pages = {244115},
	abstract = {The multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] employs a variational principle to determine an interaction potential for a CG model from simulations of an atomically detailed model of the same system. The companion paper proved that, if no restrictions regarding the form of the CG interaction potential are introduced and if the equilibrium distribution of the atomistic model has been adequately sampled, then the MS-CG variational principle determines the exact many-body potential of mean force (PMF) governing the equilibrium distribution of CG sites generated by the atomistic model. In practice, though, CG force fields are not completely flexible, but only include particular types of interactions between CG sites, e.g., nonbonded forces between pairs of sites. If the CG force field depends linearly on the force field parameters, then the vector valued functions that relate the CG forces to these parameters determine a set of basis vectors that span a vector subspace of CG force fields. The companion paper introduced a distance metric for the vector space of CG force fields and proved that the MS-CG variational principle determines the CG force force field that is within that vector subspace and that is closest to the force field determined by the many-body PMF. The present paper applies the MS-CG variational principle for parametrizing molecular CG force fields and derives a linear least squares problem for the parameter set determining the optimal approximation to this many-body PMF. Linear systems of equations for these CG force field parameters are derived and analyzed in terms of equilibrium structural correlation functions. Numerical calculations for a one-site CG model of methanol and a molecular CG model of the EMIM^+/NO_3^- ionic liquid are provided to illustrate the method. �2008 American Institute of Physics},

}

@book{Golub:1996,
	author = {Golub, G H and Van Loan, C F},
	title = {Matrix Computations, 3rd Edition},
	publisher = {Johns Hopkins University Press, Baltimore},
	year = 1996,

}

@article{Limbach:2006,
	author = {Hans-J{\"o}rg Limbach and Axel Arnold and Bernward A. Mann and Christian
	Holm},
	title = {{ESPResSo} -- An Extensible Simulation Package for Research on Soft
	Matter Systems},
	journal = {Computer Physics Communications},
	year = {2006},
	volume = {174},
	number = {9},
	pages = {704--727},
	month = may,
	doi = {10.1016/j.cpc.2005.10.005},

}

@article{SPCE,
	author = {P. G. Kusalik and I. M. Svishchev},
	title = {The spatial structure in liquid water},
	journal = {Science},
	year = {1994},
	volume = {65},
	pages = {1219-1221},

}

@article{SPCE2,
	author = {H. J. C. Berendsen and J. R. Grigera and T. P. Straatsma},
	title = {The missing term in effective pair potentials},
	journal = {J. Phys. Chem.},
	year = {1987},
	volume = {91},
	pages = {6269-6271},

}

@article{gromacs4,
	author = {Hess, Berk and Kutzner, Carsten and van der Spoel, David and Lindahl,
   Erik},
	title = {GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
   molecular simulation},
	journal = {J. Chem. Theo. Comp.},
	year = {2008},
	volume = {4},
	number = {3},
	pages = {435-447},
	doi = {10.1021/ct700301q},
	issn = {1549-9618}
}

@article{Toth:2007,
	author = {Toth, G},
	title = {Effective potentials from complex simulations: a potential-matching algorithm and remarks on coarse-grained potentials},
	journal = {J. Phys. Cond. Mat.},
	year = 2007,
	volume = {19},
	number = 33,
	pages = {335222},
	doi = {10.1088/0953-8984/19/33/335222},
	abstract = {The projection of complex interactions onto simple distance-dependent or angle-dependent classical mechanical functions is a long-standing theoretical challenge in the field of computational sciences concerning biomolecules, colloids, aggregates and simple systems as well. The construction of an effective potential may be based on theoretical assumptions, on the application of fitting procedures on experimental data and on the simplification of complex molecular simulations. Recently, a force-matching method was elaborated to project the data of Car-Parrinello ab initio molecular dynamics simulations onto two-particle classical interactions ( Izvekov et al 2004 J. Chem. Phys. 120 10896). We have developed a potential-matching algorithm as a practical analogue of this force-matching method. The algorithm requires a large number of configurations (particle positions) and a single value of the potential energy for each configuration. We show the details of the algorithm and the test calculations on simple systems. The test calculation on water showed an example in which a similar structure was obtained for qualitatively different pair interactions. The application of the algorithm on reverse Monte Carlo configurations was tried as well.

We detected inconsistencies in a part of our calculations. We found that the coarse graining of potentials cannot be performed perfectly both for the structural and the thermodynamic data. For example, if one applies an inverse method with an input of the pair-correlation function, it provides energetics data for the configurations uniquely. These energetics data can be different from the desired ones obtained by all atom simulations, as occurred in the testing of our potential-matching method.},

}

@article{Hess:2006,
	author = {Berk Hess and Christian Holm and Nico van der Vegt},
	title = {Modeling Multibody Effects in Ionic Solutions with a Concentration Dependent Dielectric Permittivity},
	journal = {Phys. Rev. Lett.},
	year = 2006,
	volume = {96},
	pages = {147801},

}

@article{Lyubartsev:2007,
	author = {Lyubartsev, A},
	title = {Multiscale modeling of lipids and lipid assemblies},
	journal = {Phys.  Chem. Liq.},
	year = 2007,
	volume = {149},
	pages = {S32-S32},
	doi = {10.1016/j.chemphyslip.2007.06.072},

}

@article{Harmandaris:2006,
	author = {Harmandaris, VA and Adhikari, NP and van der Vegt, NFA and Kremer, K},
	title = {Hierarchical modeling of polystyrene: From atomistic to coarse-grained simulations},
	journal = {Macromolecules},
	year = 2006,
	volume = {39},
	number = 19,
	pages = {6708-6719},
	doi = {10.1021/ma0606399},
	abstract = {We present a hierarchical approach that combines atomistic and mesoscopic simulations that can generally be applied to vinyl polymers. As a test case, the approach is applied to atactic polystyrene (PS). First, a specific model for atactic PS is chosen. The bonded parameters in the coarse-grained force field, based on data obtained from atomistic simulations of isolated PS dimers, are chosen in a way which allows to differentiate between meso and racemic dyads. This approach in principle allows to study isotactic and syndiotactic melts as well. Nonbonded interactions between coarse-grained beads were chosen as purely repulsive. The proposed mesoscopic model reproduces both the local structure and the chain dimensions properly. An explicit time mapping is performed, based on the atomistic and CG mean-square displacements of short chains, demonstrating an effective speed up of about 3 orders of magnitude compared to brute force atomistic simulations. Finally the equilibrated coarse-grained chains are back mapped onto the atomistic systems. This opens new routes for obtaining well equilibrated high molecular weight polymeric systems and also providing very long dynamic trajectories at the atomistic level for these polymers.},

}

@article{Villa:2009,
	author = {Villa, A and van der Vegt, NFA and Peter, C},
	title = {Self-assembling dipeptides: including solvent degrees of freedom in a coarse-grained model},
	journal = {Phys. Chem. Chem. Phys.},
	year = 2009,
	volume = {11},
	number = 12,
	pages = {2068-2076},
	keywords = {molecular-dynamics simulations, linear constraint solver, force-field, membrane-proteins, peptides, potentials, parallel, systems, design, scale},
	doi = {10.1039/b818146m},
	abstract = {In the previous paper [A. Villa, C. Peter, N. F. A. van der Vegt, Phys. Chem. Chem. Phys., 2009, DOI: 10.1039/b818144f], a strategy to develop a solvent-free coarse-grained model for peptides is outlined which is based on an atomistic (force field) description. The coarse-grained model is designed such that it correctly captures the conformational. exibility of the molecules and reproduces the interaction between peptides in aqueous solution. In the present paper, we revisit this model and present a method to devise nonbonded interactions such that also the coarse-grained level maintains explicit solvent degrees of freedom. In this new approach we rely on a structure-based coarse graining methodology which preserves the solvation structure around the peptides in combination with a method to devise nonbonded potentials between peptide beads in a way that the peptide-peptide interaction in water is represented correctly and that results in the correct thermodynamic association behavior. The outlined coarse graining strategy provides us with two (one implicit-and one explicit-solvent) models that are well suited for multiscale-simulation and scale-bridging purposes. We show that this is a powerful tool to efficiently simulate long time-scale and large length-scale biomolecular processes such as peptide self-assembly. In combination with an efficient backmapping methodology we can obtain well-equilibrated atomistic structures of the resulting aggregates.},

}

@book{Baschnagel:2000,
	author = {J. Baschnagel and K. Binder and P. Doruker and A. A. Gusev and O. Hahn and K. Kremer and W. L. Mattice and F. M{\"u}ller-Plathe and M. Murat and W. Paul and S. Santos and U. W. Suter and V. Tries},
	title = {Advances in Polymer Science: Viscoelasticity, Atomistic Models, Statistical Chemistry},
	publisher = {Springer Verlag},
	year = 2000,
	address = {Heidelberg},

}

@article{Yelash:2006,
	author = {Yelash, L. and M{\"u}ller, M. and Wolfgang, P. and Binder, K.},
	title = {How Well Can Coarse-Grained Models of Real Polymers Describe Their Structure? The Case of Polybutadiene},
	journal = {J. Chem. Theor. Comp.},
	year = 2006,
	volume = {2},
	number = 3,
	pages = {588-597},

}

@article{Nezbeda:1997,
	author = {Nezbeda, I and Slovak, J},
	title = {A family of primitive models of water: Three-, four and five-site models},
	journal = {Mol. Phys.},
	year = 1997,
	volume = {90},
	number = 3,
	pages = {353-372},
	abstract = {A family of primitive models of water, which differ from one another in the number and location of interaction sites, is introduced and their properties examined by Monte Carlo simulations. In addition to the existing symmetric 5-site model, which has its origin in the ST2 potential, asymmetric 3- and 4-site descendants of TIPS potentials are introduced along with an extended 5-site model which incorporates a short-range repulsion between the like sites. The structure of the fluids defined by the primitive models has been investigated in detail by computing site-site correlation functions, both at high and low densities, and the angular distribution of particles engaged in hydrogen bonding. For completeness, the thermodynamic properties have also been computed. It transpires that the extended 5-site model, due to its enlarged range of the hydrogen bond interaction, clearly is much better than all the other models. It is able to reproduce even semi-quantitatively the structure of real water, and thus seems well suited to all potential applications involving water, including perturbation theories using the extended model as a reference fluid.},

}

@article{Jorgensen:1998,
	author = {Jorgensen, WL and Tirado-Rives, J},
	title = {Development of the OPLS-AA force field for organic and biomolecular systems.},
	journal = {J. Chem. Soc., Abstr.},
	year = 1998,
	volume = {216},
	pages = {U696-U696},
	month = {23},

}

@article{Jorgensen:2005,
	author = {Jorgensen, WL and Tirado-Rives, J},
	title = {Potential energy functions for atomic-level simulations of water and organic and biomolecular systems},
	journal = {Proc. Natl. Acad. Sci.},
	year = 2005,
	volume = {102},
	number = 19,
	pages = {6665-6670},
	doi = {10.1073/pnas.0408037102},
	abstract = {An overview is provided on the development and status of potential energy functions that are used in atomic-level statistical mechanics and molecular dynamics simulations of water and of organic and biomolecular systems. Some topics that are considered are the form of force fields, their parameterization and performance, simulations of organic liquids, computation of free energies of hydration, universal extension for organic molecules, and choice of atomic charges. The discussion of water models covers some history, performance issues, and special topics such as nuclear quantum effects.},

}

@article{Noid:2007,
	author = {Noid, WG and Chu, JW and Ayton, GS and Voth, GA},
	title = {Multiscale coarse-graining and structural correlations: Connections to liquid-state theory},
	journal = {J. Phys. Chem. B},
	year = 2007,
	volume = {111},
	number = 16,
	pages = {4116-4127},
	month = {APR},
	doi = {10.1021/jp068549t},
	abstract = {A statistical mechanical framework elucidates the significance of structural correlations between coarse-grained (CG) sites in the multiscale coarse-graining (MS-CG) method (Izvekov, S.; Voth, G. A. J. Phys. Chem. B 2005, 109, 2469; J. Chem. Phys. 2005, 123, 134105). If no approximations are made, then the MS-CG method yields a many-body multidimensional potential of mean force describing the interactions between CG sites. However, numerical applications of the MS-CG method typically employ a set of pair potentials to describe nonbonded interactions. The analogy between coarse-graining and the inverse problem of liquid-state theory clarifies the general significance of three-particle correlations for the development of such CG pair potentials. It is demonstrated that the MS-CG methodology incorporates critical three-body correlation effects and that, for isotropic homogeneous systems evolving under a central pair potential, the MS-CG equations are a discretized representation of the well-known Yvon-Born-Green equation. Numerical calculations validate the theory and illustrate the role of these structural correlations in the MS-CG method.},

}

@article{Wallqvist:2007,
	author = {Anders Wallqvist and Raymond D. Mountain},
	title = {Molecular Models of Water: Derivation and Description},
	journal = {Rev. Comp. Chem.},
	year = 2007,
	volume = {13},
	pages = {183-247},
	doi = {10.1002/9780470125908.ch4},

}

@article{Murtola:2007,
	author = {Murtola, T and Falck, E and Karttunen, M and Vattulainen, I},
	title = {Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints},
	journal = {J. Chem. Phys.},
	year = 2007,
	volume = {126},
	number = 7,
	pages = {075101},
	doi = {10.1063/1.2646614},
	abstract = {The authors introduce a coarse-grained (CG) model for a lipid membrane comprised of phospholipids and cholesterol at different molar concentrations, which allows them to study systems that are approximately 100 nm in linear size. The systems are studied in the fluid phase above the main transition temperature. The effective interactions for the CG model are extracted from atomic-scale molecular dynamics simulations using the inverse Monte Carlo (IMC) technique, an approach similar to the one the authors used earlier to construct another CG bilayer model [T. Murtola , J. Chem. Phys. 121, 9156 (2004)]. Here, the authors improve their original CG model by employing a more accurate description of the molecular structure for the phospholipid molecules. Further, they include a thermodynamic constraint in the IMC procedure to yield area compressibilities in line with experimental data. The more realistic description of the molecular structure of phospholipids and a more accurate representation of the interaction between cholesterols and phospholipid tails are shown to improve the behavior of the model significantly. In particular, the new model predicts the formation of denser transient regions in a pure phospholipid system, a finding that the authors have verified through large scale atomistic simulations. They also find that the model predicts the formation of cholesterol-rich and cholesterol-poor domains at intermediate cholesterol concentrations, in agreement with the original model and the experimental phase diagram. However, the domains observed here are much more distinct compared to the previous model. Finally, the authors also explore the limitations of the model, discussing its advantages and disadvantages. (c) 2007 American Institute of Physics.},

}

@article{Murtola:2004,
	author = {Murtola, T and Falck, E and Patra, M and Karttunen, M and Vattulainen, I},
	title = {Coarse-grained model for phospholipid/cholesterol bilayer},
	journal = {J. Chem. Phys.},
	year = 2004,
	volume = {121},
	number = 18,
	pages = {9156-9165},
	keywords = {molecular-dynamics simulations, dissipative particle dynamics, lipid-bilayers, lateral diffusion, electrostatic interactions, structural evolution, biological-membranes, constant-pressure, phase-equilibria, cell-membranes},
	doi = {10.1063/1.1803537},
	abstract = {We construct a coarse-grained (CG) model for dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayers and apply it to large-scale simulation studies of lipid membranes. Our CG model is a two-dimensional representation of the membrane, where the individual lipid and sterol molecules are described by pointlike particles. The effective intermolecular interactions used in the model are systematically derived from detailed atomic-scale molecular dynamics simulations using the Inverse Monte Carlo technique, which guarantees that the radial distribution properties of the CG model are consistent with those given by the corresponding atomistic system. We find that the coarse-grained model for the DPPC/cholesterol bilayer is substantially more efficient than atomistic models, providing a speedup of approximately eight orders of magnitude. The results are in favor of formation of cholesterol-rich and cholesterol-poor domains at intermediate cholesterol concentrations, in agreement with the experimental phase diagram of the system. We also explore the limits of the coarse-grained model, and discuss the general validity and applicability of the present approach. (C) 2004 American Institute of Physics.},

}

@article{Muller-Plathe:2002,
	author = {M{\"u}ller-Plathe, F},
	title = {Coarse-graining in polymer simulation: From the atomistic to the mesoscopic scale and back},
	journal = {Chem. Phys. Phys. Chem.},
	year = 2002,
	volume = {3},
	number = 9,
	pages = {754-769},
	abstract = {Polymers can be theoretically and computationally described by models pertaining to different length scales and corresponding time scales. These models have traditionally been used independently of each other. Recently, considerable progress has been made In systematically linking models of different scales. This Review focuses on the generation of lattice and off-lattice coarse-grained polymer models, whose "monomers" correspond to roughly a chemical repeat unit, from chemically detailed atomistic simulations of the same polymers. Computational methods are described as well as applications to polymers in the melt and in solution. The success of multiscale simulations in solving real-world polymer problems that could not be solved in any other way suggests that they will have an important role to play in the future.},

}

@article{Feng:2009,
	author = {Feng, XL and Marcon, V and Pisula, W and Hansen, MR and Kirkpatrick, J and Grozema, F and Andrienko, D and Kremer, K and M\"ullen, K},
	title = {Towards high charge-carrier mobilities by rational design of the shape and periphery of discotics},
	journal = {Nat. Mat.},
	year = 2009,
	volume = {8},
	number = 5,
	pages = {421-426},
	doi = {10.1038/NMAT2427},
	abstract = {Discotic liquid crystals are a promising class of materials for molecular electronics thanks to their self-organization and charge transporting properties. The best discotics so far are built around the coronene unit and possess six-fold symmetry. In the discotic phase six-fold-symmetric molecules stack with an average twist of 30 degrees, whereas the angle that would lead to the greatest electronic coupling is 60 degrees. Here, a molecule with three-fold symmetry and alternating hydrophilic/hydrophobic side chains is synthesized and X-ray scattering is used to prove the formation of the desired helical microstructure. Time-resolved microwave-conductivity measurements show that the material has indeed a very high mobility, 0 : 2 cm(2) V(-1)s(-1). The assemblies of molecules are simulated using molecular dynamics, confirming the model deduced from X-ray scattering. The simulated structures, together with quantum-chemical techniques, prove that mobility is still limited by structural defects and that a defect-free assembly could lead to mobilities in excess of 10 cm(2) V(-1)s(-1).},

}

@article{Kirkpatrick:2007,
	author = {Kirkpatrick, J and Marcon, V and Nelson, J and Kremer, K and Andrienko, D},
	title = {Charge mobility of discotic mesophases: A multiscale quantum and classical study},
	journal = {Phys. Rev. Lett.},
	year = 2007,
	volume = {98},
	number = 22,
	pages = {227402},
	doi = {10.1103/PhysRevLett.98.227402},
	abstract = {A correlation is established between the molecular structure and charge mobility of discotic mesophases of hexabenzocoronene derivatives by combining electronic structure calculations, molecular dynamics, and kinetic Monte Carlo simulations. It is demonstrated that this multiscale approach can provide an accurate ab initio description of charge transport in organic materials.},

}

@article{Wang:2009,
	author = {Wang, H and Junghans, C and Kremer, K},
	title = {Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining?},
	journal = {Eur. Phys. J. E},
	year = 2009,
	volume = {28},
	number = 2,
	pages = {221-229},
	keywords = {dissipative particle dynamics, liquid water, molecular-dynamics, computer-simulations, potential functions, fluctuating charge, polarizable model, package, gromacs, systems},
	doi = {10.1140/epje/i2008-10413-5},
	abstract = {We employ the inverse Boltzmann method to coarse-grain three commonly used three-site water models (TIP3P, SPC and SPC/E) where one molecule is replaced with one coarse-grained particle with isotropic two-body interactions only. The shape of the coarse-grained potentials is dominated by the ratio of two lengths, which can be rationalized by the geometric constraints of the water clusters. It is shown that for simple two-body potentials either the radial distribution function or the geometrical packing can be optimized. In a similar way, as needed for multiscale methods, either the pressure or the compressibility can be fitted to the all atom liquid. In total, a speed-up by a factor of about 50 in computational time can be reached by this coarse-graining procedure.},

}

@article{Henderson:1974,
	author = {Henderson, RL},
	title = {UNIQUENESS THEOREM FOR FLUID PAIR CORRELATION-FUNCTIONS},
	journal = {Phys. Lett. A},
	year = 1974,
	volume = {A 49},
	number = 3,
	pages = {197-198},

}

@article{Junghans:2008,
	author = {Junghans, C and Praprotnik, M and Kremer, K},
	title = {Transport properties controlled by a thermostat: An extended dissipative particle dynamics thermostat},
	journal = {Soft Matter},
	year = 2008,
	volume = {4},
	number = 1,
	pages = {156-161},
	keywords = {coarse-grained simulations, activated rate-processes, molecular-dynamics, computer-simulations, polymer melts, constant, equation, systems, hydrodynamics, temperature},
	doi = {10.1039/b713568h},
	abstract = {We introduce a variation of the dissipative particle dynamics (DPD) thermostat that allows for controlling transport properties of molecular fluids. The standard DPD thermostat acts only on a relative velocity along the interatomic axis. Our extension includes the damping of the perpendicular components of the relative velocity, whilst keeping the advantages of conserving Galilei invariance and within our error bar also hydrodynamics. This leads to a second friction parameter for tuning the transport properties of the system. Numerical simulations of a simple Lennard-Jones fluid and liquid water demonstrate a very sensitive behaviour of the transport properties, e. g., viscosity, on the strength of the new friction parameter. We envisage that the new thermostat will be very useful for the coarse-grained and adaptive resolution simulations of soft matter, where the diffusion constants and viscosities of the coarse-grained models are typically too high/low, respectively, compared to all-atom simulations.},

}

@book{Janke:2002,
	author = {Wolfhard Janke},
	title = {Statistical Analysis of Simulations: Data Correlations and Error Estimation},
	year = {2002},
	editor = {J. Grotendorst and D. Marx and A. Muramatsu},
	volume = {10},
	series = {NIC Series, From Theory to Algorithms, Lecture Notes},
	pages = {423-445}
}

@article{Leon:2005,
	author = {Leon, S and van der Vegt, N and Delle Site, L and Kremer, K},
	title = {Bisphenol A polycarbonate: Entanglement analysis from coarse-grained MD simulations},
	journal = {Macromolecules},
	year = 2005,
	volume = {38},
	number = 19,
	pages = {8078-8092},
	month = {SEP},
	keywords = {tg amorphous polymers, hydrogenated polybutadiene, computer-simulations, chain entanglement, molecular-weights, melts, dynamics, diffusion, reptation, viscosity},
	abstract = {Simulation data are presented for a coarse-grained model of polycarbonate (BPA-PC), which allow for a detailed comparison of different ways to study the chain dynamics and predict the entanglement molecular weight. Most of the standard experimental quantities are determined for the very same set of systems and thus provide an opportunity for a detailed comparison of data far beyond typical experiments or simulations. By employing a suitably coarse-grained model, which still contains the essentials of the BPA-PC structure, simulation times compared to atomistic simulations could be extended by several orders of magnitude, reaching well into the characteristic experimental regime. We find that a recently developed topological entanglement analysis compares well with a direct determination of the modulus from simulations as with experiments on well-characterized samples. This confirms the extraordinarily small value of the entanglement molecular weight on M-e between 1200 and 1400 corresponding to N-e close to 5.},

}

@book{Voth:2008,
	title = {Coarse-Graining of Condensed Phase and Biomolecular Systems},
	publisher = {Taylor and Francis},
	year = {2008},
	editor = {Gregory A. Voth},

}

@article{Peter:2009,
	author = {Christine Peter and Kurt Kremer},
	title = {Multiscale simulation of soft matter systems?from the atomistic to the coarse grained level and back},
	journal = {Soft Matter},
	year = {2009},
	note = {accepted},

}

@article{Johnson:2007,
	author = {Johnson, ME and Head-Gordon, T and Louis, AA},
	title = {Representability problems for coarse-grained water potentials},
	journal = {J. Chem. Phys.},
	year = 2007,
	volume = {126},
	number = 14,
	pages = {-},
	month = {APR},
	keywords = {structural order, pair potentials, 3-body forces, liquid water, models, fluids, argon, mixtures},
	abstract = {The use of an effective intermolecular potential often involves a compromise between more accurate, complex functional forms and more tractable simple representations. To study this choice in detail, we systematically derive coarse-grained isotropic pair potentials that accurately reproduce the oxygen-oxygen radial distribution function of the TIP4P-Ew water model at state points over density ranges from 0.88 to 1.30 g/cm(3) and temperature ranges from 235 to 310 K. Although by construction these effective potentials correctly represent the isothermal compressibility of TIP4P-Ew water, they do not accurately resolve other thermodynamic properties such as the virial pressure, the internal energy, or thermodynamic anomalies. Because at a given state point the pair potential that reproduces the pair structure is unique, we have therefore explicitly demonstrated that it is impossible to simultaneously represent the pair structure and several key equilibrium thermodynamic properties of water with state-point dependent radially symmetric pair potentials. We argue that such representability problems are related to, but different from, more widely acknowledged transferability problems and discuss in detail the implications this has for the modeling of water and other liquids by coarse-grained potentials. Nevertheless, regardless of thermodynamic inconsistencies, the state-point dependent effective potentials for water do generate structural and dynamical anomalies. (c) 2007 American Institute of Physics.},

}

@inproceedings{Kremer:2000,
	author = {Kurt Kremer},
	booktitle = {Soft and fragile matter, nonequilibrium dynamics, metastability and flow},
	pages = {423-445},
	year = {2000},
	editor = {M. E. Cates and M. R. Evans},
	series = {Proceedings of NATO ASI Workshop},
	address = {Bristol, UK},
	publisher = {Institute of Physics},

}

@article{Zhou:2007,
	author = {Zhou, J and Thorpe, IF and Izvekov, S and Voth, GA},
	title = {Coarse-grained peptide modeling using a systematic multiscale approach},
	journal = {Biophys. J.},
	year = 2007,
	volume = {92},
	number = 12,
	pages = {4289-4303},
	month = {JUN},
	keywords = {molecular-dynamics simulation, force-matching method, potentials, field},
	doi = {10.1529/biophysj.106.094425},
	abstract = {A systematic new approach to derive multiscale coarse-grained (MS-CG) models has been recently developed. The approach employs information from atomistically detailed simulations to derive CG forces and associated effective potentials. In this work, the MS-CG methodology is extended to study two peptides representing distinct structural motifs, alpha-helical polyalanine and the beta-hairpin V5PGV5. These studies represent the first known application of this approach to peptide systems. Good agreement between the MS-CG and atomistic models is achieved for several structural properties including radial distribution functions, root mean-square deviation, and radius of gyration. The new MS-CG models are able to preserve the native states of these peptides within; 1 A backbone root mean-square deviation during CG simulations. The MS-CG approach, as with most coarse-grained models, has the potential to increase the length and timescales accessible to molecular simulations. However, it is also able to maintain a clear connection to the underlying atomistic-scale interactions.},

}

@article{Shelley:2001,
	author = {Shelley, JC and Shelley, MY and Reeder, RC and Bandyopadhyay, S and Klein, ML},
	title = {A coarse grain model for phospholipid simulations},
	journal = {J. Phys. Chem. B},
	year = 2001,
	volume = {105},
	number = 19,
	pages = {4464-4470},
	month = {MAY},
	keywords = {dipalmitoyl phosphatidylcholine bilayer, phase-transitions, computer-simulation, membrane-fusion, organization, mechanism, tension, lipids},
	doi = {10.1021/jp010238p},
	abstract = {A coarse grain model for phospholipids was systematically parametrized to mimic structural properties obtained from an atomistic simulation of a dimyristoylphosphatidylcholine bilayer. The model semiquantitatively reproduces the cross-sectional structure of a preassembled phospholipid bilayer obtained from an atomistic simulation; a property that was not directly fit. The model is sufficiently fast to permit the simulation of the self-assembly of the bilayer starting from a random configuration.},

}

@article{Sun:2006,
	author = {Sun, Q and Faller, R},
	title = {Systematic coarse-graining of a polymer blend: Polyisoprene and polystyrene},
	journal = {J.Chem. Theo. Comp.},
	year = 2006,
	volume = {2},
	number = 3,
	pages = {607-615},
	month = {MAY},
	keywords = {molecular-dynamics, segmental dynamics, terminal dynamics, local-structure, simulation, melts, mixtures, solvent, package, models},
	doi = {10.1021/ct600065v},
	abstract = {The Iterative Boltzmann Inversion technique ( also known as the Inverse Boltzmann Method) is generalized to polymer blends. We systematically optimize a mesoscale model against the structure of the blend. A polyisoprene-polystyrene blend is used as an example. Atomistic simulations of a blend of short chains in the miscible regime under melt conditions are taken as a starting point. We optimize the mesoscale model and study the onset of phase separation with increasing chain length. The mesoscale model phase separates at a chain length of 15 monomers where it was optimized, whereas the atomistic model shows only a preference of chains to aggregate to neighborhoods of like chains. We discuss the differences of the optimization between a blend and a homopolymer system in detail.},

}

@article{Shih:2006,
	author = {Shih, AY and Arkhipov, A and Freddolino, PL and Schulten, K},
	title = {Coarse grained protein-lipid model with application to lipoprotein particles},
	journal = {J. Phys. Chem. B},
	year = 2006,
	volume = {110},
	number = 8,
	pages = {3674-3684},
	month = {MAR 2},
	keywords = {apolipoprotein-a-i, high-density-lipoproteins, molecular-dynamics simulations, belt model, membrane-proteins, minimalist model, bilayers, cytochrome-p450, vesicles, phase},
	doi = {10.1021/jp0550816},
	abstract = {A coarse-grained model for molecular dynamics simulations is extended from lipids to proteins. In the framework of such models pioneered by Klein, atoms are described group-wise by beads, with the interactions between beads governed by effective potentials. The extension developed here is based on a coarse-grained lipid model developed previously by Marrink et al., although future versions will reconcile the approach taken with the systematic approach of Klein and other authors. Each amino acid of the protein is represented by two coarse-grained beads, one for the backbone (identical for all residues) and one for the side-chain (which differs depending on the residue type). The coarse-graining reduces the system size about 10-fold and allows integration time steps of 25-50 fs. The model is applied to simulations of discoidal high-density lipoprotein particles involving water, lipids, and two primarily helical proteins. These particles are an ideal test system for the extension of coarse-grained models. Our model proved to be reliable in maintaining the shape of preassembled particles and in reproducing the overall structural features of high-density lipoproteins accurately. Microsecond simulations of lipoprotein assembly revealed the formation of a protein-lipid complex in which two proteins are attached to either side of a discoidal lipid bilayer.},

}

@article{Chayes:1984b,
	author = {Chayes, JT and Chayes, L and Lieb, EH},
	title = {THE INVERSE PROBLEM IN CLASSICAL STATISTICAL-MECHANICS},
	journal = {Comm. Math. Phys.},
	year = 1984,
	volume = {93},
	number = 1,
	pages = {57-121},

}

@article{Chayes:1984a,
	author = {Chayes, JT and Chayes, L},
	title = {ON THE VALIDITY OF THE INVERSE CONJECTURE IN CLASSICAL DENSITY FUNCTIONAL THEORY},
	journal = {J. Stat. Phys.},
	year = 1984,
	volume = {36},
	pages = {471-488},

}

@article{Nose:1984,
  	author = { Nos{\'e}, S},
	title = {A molecular dynamics method for simulations in the canonical ensemble},
	journal = {Mol. Phys.},
	year = 1984,
	volume = 52,
	pages = {255-268}
}


@article{Gunster:1988,
	title = {A Leap-frog Algorithm for Stochastic Dynamics},
	volume = {1},
	number = {3},
	journal = {Mol. Sim.},
	author = {W. F. Van Gunsteren and H. J. C. Berendsen},
	year = {1988},
	pages = {173}
}

@article{Hoover:1985,
	title = {Canonical dynamics: Equilibrium phase-space distributions},
	volume = {31},
	shorttitle = {Canonical dynamics},
	number = {3},
	journal = {Phys. Rev. A},
	author = {William G. Hoover},
	year = {1985},
	pages = {1695}
}

@article{ Harmandaris:2007,
Author = {Harmandaris, Vagelis A. and Reith, Dirk and Van der Vegt, Nico F. A. and Kremer, Kurt},
Title = {Comparison between coarse-graining models for polymer systems: Two mapping schemes for polystyrene},
Journal = {Macromol. Chem. Phys.},
Year = {2007},
Volume = {208},
Number = {19-20},
Pages = {2109-2120}
}

@article{ Villa:2009b,
Author = {Villa, Alessandra and Peter, Christine and van der Vegt, Nico F. A.},
Title = {{Self-assembling dipeptides: conformational sampling in solvent-free
   coarse-grained simulation}},
Journal = {Phys. Chem. Chem. Phys.},
Year = {2009},
Volume = {11},
Number = {12},
Pages = {2077-2086}
}


@article{ Lyubartsev:2005,
	Author = {Lyubartsev, AP},
	Title = {Multiscale modeling of lipids and lipid bilayers},
	Journal = {Eur. Biophys. J.},
	Year = {2005},
	Volume = {35},
	Number = {1},
	Pages = {53-61}
}

@article{ Fritz:2009,
Author = {Fritz, Dominik and Harmandaris, Vagelis A. and Kremer, Kurt and van der Vegt, Nico F. A.},
Title = {Coarse-Grained Polymer Melts Based on Isolated Atomistic Chains: Simulation of Polystyrene of Different Tacticities},
Journal = {Macromolecules},
Year = {2009},
Volume = {42},
Number = {19},
Pages = {7579-7588}
}

@article{Ganguly:2012,
  author    = {Ganguly, P. and Mukherji, D. and Junghans, C. and van der Vegt, Nico F. A.},
  title     = {Kirkwood-Buff coarse-grained force fields for aqueous solutions},
  journal   = {J. Chem. Theor. Comp.},
  year      = {2012},
  volume    = {},
  pages     = {accepted},
  condmat   = {},
  doi       = {10.1021/ct3000958},
  abstract  = {}
}
